The trilogy has concluded 2 years ago with another addition to the story being on the way in the near or distant future, yet I can't help but feel that quite a few questions have been left unanswered in the story.
So I asked myself what seems to be the most reasonable explanation to these unanswered questions, to both me and the rest of the Mass Effect community.
The Female Krogan and the Tuchanka Bomb[]
How exactly did Cerberus find about Bakara on Sur'Kesh and the turian bomb on Tuchanka? The female krogan is being kept on a top secret salarian base and the bomb has been buried for over a thousand years and kept just as much of a secret, yet Cerberus just happens to know where to look for them? Yes I know that there was a passing mention of a salarian traitor that contacted them, but the game never even explained any more than that.
I believe that Dalatrass Linron was the one who contacted them, if not directly then she ordered some minion loyal to her to contact them. I mean, not only does she have access to extremely classified information Linron also has the motivation of wanting the entire krogan race to die off simply because she believes they're nothing more than a race of dumb, savage animals that need to be put down, regardless of the devastating effect it'd have on the Reaper War.
The Catalyst[]
Why does the Catalyst believe that melting people into goo to be turned into Reapers was the best way to preserve organic life? How come its entire logic comes off as incredibly flawed even though better alternatives have been proven to exist? How was it able to appear as the little brat that gets blown up at the beginning of the game?
Simple: The Catalyst isn't a true AI,; by appearances, it is little more than a VI, somewhere between the extremely simple Avina and the incredibly complex Vendetta and Vigil. The Leviathans merely programmed it with a single order "preserve life by any means necessary", any AI or extremely complex VI would likely have not been so literal (and can actually be reasoned with) whereas a simple VI like Avina does not know of the Purgatory Bar and instead confuses it with the location in religion (and cannot be reasoned with due programming). The Catalyst is more along the line of the latter.
As for why it showed up looking exactly like the kid, it's been shown on the derelict Reaper that they're able to look through minds when the crew members were sharing memories. If the kid wasn't a product of the beginning of Reaper indoctrination, then it isn't too much of a stretch that the Catalyst and Reapers have been looking through Shep's memories for a specific person.
Rana and The Illusive Man[]
This one confused me a lot. I mean, in both of her appearances, regardless of how short they were, she showed absolutely no signs of being indoctrinated. Yet by the third game we get an email on how she's been indoctrinated all along and killed herself and several military officials. How did this get past us? And the Illusive Man too, he's been touched by the Reapers' decades before it even started, yet which of his actions were his own and which of them were caused by the Reaper's influence? We all know that any individual who is in proximity of any form of Reaper tech becomes more and more indoctrinated the longer they are near it. But that doesn't explain how people who were near the devices were able to look like they're unaffected only to suddenly reveal that they've been indoctrinated with little to no warning.
I kind of believe that anyone that has been in such proximity with a Reaper device but not long enough to any actual signs of indoctrination at least sometime before or during the energy pulse (the ones from Object Rho and the Shanxi object for TIM being examples), it plants a seed of sorts into their minds so that when the Reapers arrived the seeds sprout and rapidly indoctrinate them. Or, alternatively, the "seed" slowly works its way through its victim's mind even without any close proximity to Reapers, going completely unnoticed until the Reapers' arrival where said indoctrination takes control of them.
Missing Ammo Types[]
In the first game we had many types of ammunition we could possibly choose from, in addition to Armor-Piercing, Incendiary, Cryo, Disruptor and Warp ammo we use now, we used to have Anti-Personnel, High Explosive, Shield Piercing, High Impact, Toxic and Radioactive rounds. But they were removed entirely from standard gameplay with little to no in-universe explanation. Why is that?
My belief is that they were all declared illegal in Citadel space, like the use of the three edged knives in real life, because they were too powerful. I mean, ammunition that renders the most powerful shielding irrelevant by bypassing them completely, ammunition that basically turns all rounds into grenades, etc. And with the "Geth Attack" on the Citadel, they also became almost useless against what was believed to be the next big threat. So the Council likely decided to cease all production (or prohibit all vendors from selling them in Citadel space), or in the case of phasic and high explosive ammo, put a lot of restrictions on them, so that they can focus their research on making anti-synthetic weaponry such as Disruptor ammo. Shepard was only able get access to these in the first game because as a Spectre, Shepard doesn't need to adhere to any conventions of combat and use them freely; and Thane, being an assassin, was able to acquire Shredder ammunition for his job.
Thermal Clips[]
They say that Thermal Clips were put into production in order to win firefights, with the victor decided as being the one who can fire the most rounds the fastest without any worry of overheating weaponry. However, there are multiple flaws with this explanation. The first is that having to conserve shots in thermal clips is completely counterproductive to the purpose of firing the most rounds the fastest; the second is that weapons are unable to fire without thermal clips, which would be problematic during extended firefights or long missions where one could run low on them (such as the mission on Aeia were it not for gameplay reasons); and the third is that a good weapon with high level cooling upgrades would render thermal clips completely pointless. So why would weapon manufacturers invest in thermal clips if they just created the problem of limited ammo that mass effect technology was supposed to have solved in the first place?
Simple, because they weren't meant to solve the problem of heat management, they were adapted into weapons because of the prevalent use of Sabotage. If I recall correctly, a sabotaged weapon takes much longer to cool down than a weapon that overheated through standard gunfire, which is why Geth Hoppers and Pinnacle Station's simulation of the First Contact War are so difficult (and they keep using it all the time). With thermal clips, any user of a weapon that's hit with sabotage could just simply eject the clip and keep firing; but of course, all technology advances with time which is why overload and later sabotage are able to fry them, they're not targeting the heat management for the firing mechanism like back in the first game, those powers are targeting other systems independent of the thermal clips to make weapons overheat and Sabotage is hacking the weapon systems in order to electrocute its wielder.
(More will be added later)